Does + Eigen gene mean + overal module gene expression?
library(tidyverse)
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package ‘ggplot2’ was built under R version 3.5.2package ‘tibble’ was built under R version 3.5.2package ‘tidyr’ was built under R version 3.5.2package ‘purrr’ was built under R version 3.5.2package ‘dplyr’ was built under R version 3.5.2package ‘stringr’ was built under R version 3.5.2package ‘forcats’ was built under R version 3.5.2[30m── [1mConflicts[22m ───────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
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library(WGCNA)
package ‘WGCNA’ was built under R version 3.5.2Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Attaching package: ‘WGCNA’
The following object is masked from ‘package:stats’:
cor
load("../output/WGCNA_UN_all.Rdata")
expr <- expr.data.UN.t %>%
scale() %>%
t() %>%
as.tibble() %>%
mutate(color=merge$colors,
ID=colnames(expr.data.UN.t)) %>%
select(ID, color, everything())
`as.tibble()` is deprecated, use `as_tibble()` (but mind the new semantics).
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expr[1:10, 1:10]
expr_MEs <- MEs %>%
scale() %>%
t() %>%
as.data.frame() %>%
rownames_to_column("ID") %>%
mutate(color=str_sub(ID, 3)) %>%
select(ID, color, everything()) %>%
bind_rows(., expr) %>%
mutate(type=ifelse(str_detect(ID, "^ME"), "eigen", "gene")) %>%
select(ID, color, type, everything())
expr_MEs
map(unique(expr_MEs$color), function(x) {
expr_MEs %>%
filter(color==x) %>%
gather(key = "RIL", value="expression", -ID, -color, -type) %>%
ggplot(aes(x=RIL, y=expression, group=ID, alpha=type, color=type )) +
geom_line() +
scale_alpha_manual(values = c("eigen" = 1, "gene" = 0.05)) +
scale_color_manual(values = c("eigen" = "red", "gene" = "black")) +
ggtitle(color)
})
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